Lehrstuhl für Biochemie
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- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg (1)
- Genelux Corporation, San Diego Science Center, 3030 Bunker Hill Street, Suite 310, San Diego, California 92109, USA (1)
- MRB Forschungszentrum für Magnet-Resonanz-Bayern e.V., Am Hubland, D-97074 Würzburg (1)
- Rudolf-Virchow-Zentrum DFG-Forschungszentrum für Experimentelle Biomedizin der Universität Würzburg (1)
Background:
Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. We previously described GLV-1h68, a modified Vaccinia Virus with exclusive tropism for tumor cells, and we observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro and its ability to colonize and eliminate tumor in vivo.
Methods:
In the current study we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines. Selected cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain. In order to identify correlates of permissity to viral infection, we measured transcriptional profiles of the cell lines prior infection.
Results:
We observed highly heterogeneous permissivity to VACV infection amongst the cell lines. The heterogeneity of permissivity was independent of tissue with the exception of B cell derivation. Cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain and a significant correlation was found suggesting a common permissive phenotype. While no clear transcriptional pattern could be identified as predictor of permissivity to infection, some associations were observed suggesting multifactorial basis permissivity to viral infection.
Conclusions:
Our findings have implications for the design of oncolytic therapies for cancer and offer insights into the nature of permissivity of tumor cells to viral infection.
Background:
Retinitis pigmentosa (RP) is an inherited eye disease characterized by the progressive degeneration of rod photoreceptor cells. Mutations in pre-mRNA splicing factors including PRPF31 have been identified as cause for RP, raising the question how mutations in general factors lead to tissue specific defects.
Results:
We have recently shown that the zebrafish serves as an excellent model allowing the recapitulation of key events of RP. Here we use this model to investigate two pathogenic mutations in PRPF31, SP117 and AD5, causing the autosomal dominant form of RP. We show that SP117 leads to an unstable protein that is mislocalized to the rod cytoplasm. Importantly, its overexpression does not result in photoreceptor degeneration suggesting haploinsufficiency as the underlying cause in human RP patients carrying SP117. In contrast, overexpression of AD5 results in embryonic lethality, which can be rescued by wild-type Prpf31. Transgenic retina-specific expression of AD5 reveals that stable AD5 protein is initially localized in the nucleus but later found in the cytoplasm concurrent with progressing rod outer segment degeneration and apoptosis. Importantly, we show for the first time in vivo that retinal transcripts are wrongly spliced in adult transgenic retinas expressing AD5 and exhibiting increased apoptosis in rod photoreceptors.
Conclusion:
Our data suggest that distinct mutations in Prpf31 can lead to photoreceptor degeneration through different mechanisms, by haploinsufficiency or dominant-negative effects. Analyzing the AD5 effects in our animal model in vivo, our data imply that aberrant splicing of distinct retinal transcripts contributes to the observed retina defects.
Telomerase, the enzyme that maintains telomeres, preferentially lengthens short telomeres. The S. cerevisiae Pif1 DNA helicase inhibits both telomerase-mediated telomere lengthening and de novo telomere addition at double strand breaks (DSB). Here, we report that the association of the telomerase subunits Est2 and Est1 at a DSB was increased in the absence of Pif1, as it is at telomeres, suggesting that Pif1 suppresses de novo telomere addition by removing telomerase from the break. To determine how the absence of Pif1 results in telomere lengthening, we used the single telomere extension assay (STEX), which monitors lengthening of individual telomeres in a single cell cycle. In the absence of Pif1, telomerase added significantly more telomeric DNA, an average of 72 nucleotides per telomere compared to the 45 nucleotides in wild type cells, and the fraction of telomeres lengthened increased almost four-fold. Using an inducible short telomere assay, Est2 and Est1 no longer bound preferentially to a short telomere in pif1 mutant cells while binding of Yku80, a telomere structural protein, was unaffected by the status of the PIF1 locus. Two experiments demonstrate that Pif1 binding is affected by telomere length: Pif1 (but not Yku80) -associated telomeres were 70 bps longer than bulk telomeres, and in the inducible short telomere assay, Pif1 bound better to wild type length telomeres than to short telomeres. Thus, preferential lengthening of short yeast telomeres is achieved in part by targeting the negative regulator Pif1 to long telomeres.
Background:
Recent studies have shown that human ferritin can be used as a reporter of gene expression for magnetic resonance imaging (MRI). Bacteria also encode three classes of ferritin-type molecules with iron accumulation properties.
Methods and Findings:
Here, we investigated whether these bacterial ferritins can also be used as MRI reporter genes and which of the bacterial ferritins is the most suitable reporter. Bacterial ferritins were overexpressed in probiotic E. coli Nissle 1917. Cultures of these bacteria were analyzed and those generating highest MRI contrast were further investigated in tumor bearing mice. Among members of three classes of bacterial ferritin tested, bacterioferritin showed the most promise as a reporter gene. Although all three proteins accumulated similar amounts of iron when overexpressed individually, bacterioferritin showed the highest contrast change. By site-directed mutagenesis we also show that the heme iron, a unique part of the bacterioferritin molecule, is not critical for MRI contrast change. Tumor-specific induction of bacterioferritin-expression in colonized tumors resulted in contrast changes within the bacteria-colonized tumors.
Conclusions:
Our data suggest that colonization and gene expression by live vectors expressing bacterioferritin can be monitored by MRI due to contrast changes.
Introduction:
Oncolytic viruses show promise for treating cancer. However, to assess therapeutic efficacy and potential toxicity, a noninvasive imaging modality is needed. This study aimed to determine if insertion of the human sodium iodide symporter (hNIS) cDNA as a marker for non-invasive imaging of virotherapy alters the replication and oncolytic capability of a novel vaccinia virus, GLV-1h153.
Methods:
GLV-1h153 was modified from parental vaccinia virus GLV-1h68 to carry hNIS via homologous recombination. GLV-1h153 was tested against human pancreatic cancer cell line PANC-1 for replication via viral plaque assays and flow cytometry. Expression and transportation of hNIS in infected cells was evaluated using Westernblot and immunofluorescence. Intracellular uptake of radioiodide was assessed using radiouptake assays. Viral cytotoxicity and tumor regression of treated PANC-1tumor xenografts in nude mice was also determined. Finally, tumor radiouptake in xenografts was assessed via positron emission tomography (PET) utilizing carrier-free (124)I radiotracer.
Results:
GLV-1h153 infected, replicated within, and killed PANC-1 cells as efficiently as GLV-1h68. GLV-1h153 provided dose-dependent levels of hNIS expression in infected cells. Immunofluorescence detected transport of the protein to the cell membrane prior to cell lysis, enhancing hNIS-specific radiouptake (P < 0.001). In vivo, GLV-1h153 was as safe and effective as GLV-1h68 in regressing pancreatic cancer xenografts (P < 0.001). Finally, intratumoral injection of GLV-1h153 facilitated imaging of virus replication in tumors via (124)I-PET.
Conclusion:
Insertion of the hNIS gene does not hinder replication or oncolytic capability of GLV-1h153, rendering this novel virus a promising new candidate for the noninvasive imaging and tracking of oncolytic viral therapy.
G-Quadruplex (G4)-Strukturen sind sehr stabile und polymorphe DNA und RNA Sekundärstrukturen mit einem konservierten Guanin-reichen Sequenzmotiv (G4-Motiv). Sie bestehen aus übereinander gestapelten planaren G-Quartetts, in denen je vier Guanine durch Wasserstoffbrückenbindungen zusammengehalten werden.
Da G4-Motive in Eukaryoten an bestimmten Stellen im Genom angereichert vorkommen, wird angenommen, dass die Funktion von G4-Strukturen darin besteht, biologische Prozesse positiv oder negativ zu regulieren. Aufgrund der hohen thermodynamischen Stabilität von G4 Strukturen ist davon auszugehen, dass Proteine in die Faltung, Stabilisierung und Entfaltung dieser Nukleinsäure-Strukturen regulatorisch involviert sind. Bis heute wurden viele Proteine in der Literatur beschrieben, die G4-Strukturen entwinden können. Jedoch konnten bisher nur wenige Proteine identifiziert werden, die in vivo die Faltung fördern oder G4-Strukturen stabilisieren.
Durch Yeast One-Hybrid (Y1H)-Screenings habe ich Zuo1 als neues G4 bindendes Protein identifiziert. In vitro Analysen bestätigten diese Interaktion und es stellte sich heraus, dass Zuo1 G4-Strukturen stabilisiert. Übereinstimmend mit den in vitro Daten konnte gezeigt werden, dass Zuo1 signifikant an G4-Motive im Genom von Saccharomyces ceresivisiae bindet. Genomweit überlappen G4-Motive, an die Zuo1 bindet, mit Stellen, an denen die DNA Replikation zum Stillstand kommt und vermehrt DNA Schäden vorkommen. Diese Ergebnisse legen nahe, dass Zuo1 eine Funktion während der DNA Reparatur oder in Zusammenhang mit dem Vorankommen der DNA Replikationsgabel hat, indem G4-Strukturen stabilisiert werden. Diese Hypothese wird außerdem durch genetische Experimente gestützt, wonach in Abwesenheit von Zuo1 die Genominstabilität zunimmt. Aufgrund dieser Daten war es möglich ein Model zu entwickeln, bei dem Zuo1 während der S-Phase G4-Strukturen bindet und stabilisiert wodurch die DNA Replikation blockiert wird. Diese Interaktion findet neben Stellen schadhafter DNA statt und unterstützt somit DNA Reparatur-Prozesse wie beispielsweise die Nukleotidexzisionsreparatur.
Als weiteres potentielles G4-bindendes Protein wurde Slx9 in Y1H-Screenings identifiziert. In vitro Experimente zeigten zwar, dass Slx9 mit höherer Affinität an G4-Strukturen bindet im Vergleich zu anderen getesteten DNA Konformationen, jedoch wurde in S. cerevisiae genomweit keine signifikante Bindung an G4-Motive festgestellt.
The formation of macromolecular complexes within the crowded environment of cells often requires aid from assembly chaperones. PRMT5 and SMN complexes mediate this task for the assembly of the common core of pre-mRNA processing small nuclear ribonucleoprotein particles (snRNPs). Core formation is initiated by the PRMT5-complex subunit pICln, which pre-arranges the core proteins into spatial positions occupied in the assembled snRNP. The SMN complex then accepts these pICln-bound proteins and unites them with small nuclear RNA (snRNA). Here, we have analyzed how newly synthesized snRNP proteins are channeled into the assembly pathway to evade mis-assembly. We show that they initially remain bound to the ribosome near the polypeptide exit tunnel and dissociate upon association with pICln. Coincident with its release activity, pICln ensures the formation of cognate heterooligomers and their chaperoned guidance into the assembly pathway. Our study identifies the ribosomal quality control hub as a site where chaperone-mediated assembly of macromolecular complexes can be initiated.
Biochemische und strukturelle Charakterisierung der Genexpressionsmaschinerie des Vaccinia Virus
(2018)
Die Familie der Pockenviren zeichnet sich durch ein komplexes DNA Genom aus und hat großes medizinisches Potential. Am eindrucksvollsten ist dies für das Vaccinia-Virus (VACV) belegt, welches nicht nur als Pocken-Impfstoff eingesetzt wird, sondern auch als onkolytisches Virus in der Tumorbiologie. VACV hat einen außergewöhnlichen Replikationszyklus, welcher ausschließlich im Zytoplasma der Wirtszelle stattfindet. Somit ist die gesamte virale Genexpressionsmaschinerie völlig unabhängig von kernvermittelten Reaktionen des Wirts und somit auch aus Sicht der Grundlagenforschung von größtem Interesse. Die Schlüsselkomponente der viralen Genexpression ist die makromolekulare DNA-abhängige RNA Polymerase (vvRPO), deren Untereinheiten allesamt Virus-kodiert sind. Zwar wurden in den letzten Jahren Protokolle zur biochemischen und funktionellen Charakterisierung der vvRPO etabliert, ein detailliertes Wissen über deren Zusammenlagerung in vivo und die räumlichen und zeitlichen Interaktionen mit den Transkriptions- bzw. Prozessierungsfaktoren sind aber weitgehend unbekannt.
Diese Arbeit umfasst Untersuchungen zur strukturellen und funktionellen Charakterisierung der vvRPO und seiner assoziierten Faktoren. Grundlage hierfür war die Etablierung eines Reinigungsprotokolls mithilfe eines neu konstruierten rekombinanten VACV (GLV-1h439). Diese Strategie erlaubte es hoch-molekulare native vvRPO Komplexe zu isolieren. Ein transkriptions-inaktiver Komplex (Komplex I) mit einer kalkulierten Masse von 575 kDa bestand aus den acht Untereinheiten des vvRPO Holoenzyms und den Polymerase-assoziierten Faktoren RAP94 und D6. Ein zweiter, transkriptionell aktiver Komplex (Komplex II) mit einer Masse von 803 kDa enthielt, neben dem Holoenzym der vvRPO, noch weitere Faktoren, die primär die Erkennung der DNA-Matrize und die Prozessierung der naszierenden RNA vermitteln. Hierbei handelt es sich um RAP94, das virale Capping Enzym bestehend aus den zwei Untereinheiten D1 und D12, A7 und dem Terminationsfaktor NPH I. Interessanterweise enthielt dieser Komplex zusätzlich mit E11 eine bislang unbekannte weitere Protein-Komponente, sowie tRNAGln und tRNAArg. Der isolierte Kompelx II ist daher ein Ribonukleoprotein (RNP).
Die Verfügbarkeit von hoch-reinen vvRPO Komplexen erlaubte es erstmals deren strukturelle Architektur zu untersuchen. Hierfür wurden drei experimentelle Ansätze, die klassische Röntgenstrukturanalyse, die Kryo-Elektronenmikroskopie (Kryo-EM) und Quervernetzungssstudien miteinander kombiniert. Die Strukturen der Komplexe I und II haben eine Auflösung von 11-12 Å, wobei auffällig war, dass beide eine markante strukturelle Ähnlichkeit zur eukaryotischen RNA Polymerase II aufwiesen. Darüber hinaus gelang es zusätzliche Bereiche im Komplex II zu definieren, welche die Polymerase-assoziierten Prozessierungsfaktoren beherbergen. Zudem konnte die atomare Struktur von E11, mittels Röntgenstrukturanalyse bei einer Auflösung von 1,9 Å, gelöst werden. Das E11 Protein besitzt ein neuartiges Faltungsmuster und weist einen intensiven Dimerisierungskontakt auf, welcher sich über vier ß-Faltblätter ausbildet.
Die im Rahmen dieser Arbeit erhaltenen Daten legen die Grundlage für ein detailliertes Verständnis der räumlichen Organisation der viralen Transkriptonsmaschinerie. Darüber hinaus werden sie funktionelle Studien ermöglichen, welche die Rolle der einzelnen Proteine, sowie der tRNAs bei der mRNA Synthese klären helfen.
G-quadruplex structures are highly stable alternative DNA structures that can, when not properly regulated, impede replication fork progression and cause genome instability (Castillo Bosch et al, 2014; Crabbe et al, 2004; Koole et al, 2014; Kruisselbrink et al, 2008; London et al, 2008; Lopes et al, 2011; Paeschke et al, 2013; Paeschke et al, 2011; Piazza et al, 2015; Piazza et al, 2010; Piazza et al, 2012; Ribeyre et al, 2009; Sabouri et al, 2014; Sarkies et al, 2012; Sarkies et al, 2010; Schiavone et al, 2014; Wu & Spies, 2016; Zimmer et al, 2016). The aim of this thesis was to identify novel G-quadruplex interacting proteins in Saccharomyces cerevisiae and to unravel their regulatory function at these structures to maintain genome integrity. Mms1 and Rtt101 were identified as G-quadruplex binding proteins in vitro via a pull-down experiment with subsequent mass spectrometry analysis. Rtt101, Mms1 and Mms22, which are all components of an ubiquitin ligase (Rtt101Mms1/Mms22), are important for the progression of the replication fork following fork stalling (Luke et al, 2006; Vaisica et al, 2011; Zaidi et al, 2008). The in vivo binding of endogenously tagged Mms1 to its target regions was analyzed genome-wide using chromatin-immunoprecipitation followed by deep-sequencing. Interestingly, Mms1 bound independently of Mms22 and Rtt101 to G-rich regions that have the potential to form G-quadruplex structures. In vitro, formation of G-quadruplex structures could be shown for the G-rich regions Mms1 bound to. This binding was observed throughout the cell cycle. Furthermore, the deletion of MMS1 caused replication fork stalling as evidenced by increased association of DNA Polymerase 2 at Mms1 dependent sites. A gross chromosomal rearrangement assay revealed that deletion of MMS1 results in a significantly increased genome instability at G-quadruplex motifs compared to G-rich or non-G-rich regions. Additionally, binding of the helicase Pif1, which unwinds G4 structures in vitro (Paeschke et al, 2013; Ribeyre et al, 2009; Sanders, 2010; Wallgren et al, 2016), to Mms1 binding sites was reduced in mms1 cells. The data presented in this thesis, together with published data, suggests a novel mechanistic model in which Mms1 binds to G-quadruplex structures and enables Pif1 association. This allows for replication fork progression and genome integrity.
The Epstein-Barr Virus (EBV) -encoded EBNA2 protein, which is essential for the in vitro transformation of B-lymphocytes, interferes with cellular processes by binding to proteins via conserved sequence motifs. Its Arginine-Glycine (RG) repeat element contains either symmetrically or asymmetrically di-methylated arginine residues (SDMA and ADMA, respectively). EBNA2 binds via its SDMA-modified RG-repeat to the survival motor neurons protein (SMN) and via the ADMA-RG-repeat to the NP9 protein of the human endogenous retrovirus K (HERV-K (HML-2) Type 1). The hypothesis of this work was that the methylated RG-repeat mimics an epitope shared with cellular proteins that is used for interaction with target structures. With monoclonal antibodies against the modified RG-repeat, we indeed identified cellular homologues that apparently have the same surface structure as methylated EBNA2. With the SDMA-specific antibodies, we precipitated the Sm protein D3 (SmD3) which, like EBNA2, binds via its SDMA-modified RG-repeat to SMN. With the ADMA-specific antibodies, we precipitated the heterogeneous ribonucleoprotein K (hnRNP K). Specific binding of the ADMA-antibody to hnRNP K was demonstrated using E. coli expressed/ADMA-methylated hnRNP K. In addition, we show that EBNA2 and hnRNP K form a complex in EBV-infected B-cells. Finally, hnRNP K, when co-expressed with EBNA2, strongly enhances viral latent membrane protein 2A (LMP2A) expression by an unknown mechanism as we did not detect a direct association of hnRNP K with DNA-bound EBNA2 in gel shift experiments. Our data support the notion that the methylated surface of EBNA2 mimics the surface structure of cellular proteins to interfere with or co-opt their functional properties.